Goal:

Think, explore, & write about what the co-evolutionary interaction between newts & snakes with different genetic architectures (GAs, combination of mutation rate & mutation effect size). This markdown is investigating what happens to the newt and snake population when I increase the interaction rate.

Questions:

How does changing the interaction rate affect the survival of the newt or snake population? Is there a change in the spatial phenotype correlation? Does the interaction rate lead to different phenotype outcome (typical interaction rate is 0.05)? What does changing the interaction rate mean in order of how many snakes encounter a newt in their lifetime?

Experiment

I created a simulation study to observe the co-evolutionary outcome of the newt-snake interaction with different genetic architectures (GAs) in a spatial setting. I hypothesized that we would see an interaction (co-evolutionary arms race) between newt and snake phenotype under some GA combinations when newts and snakes were evolving over geographical space. Each GA is paired with another GA creating 16 combinations.

GA1 experiment values:

Landscape: A tall map!: 35*4 H, 35 W

I tested different interaction rates:

Each GA combination, trial, and interaction rate has its own msprime simulation.

Sometimes a higher interaction rate will lead to a species extinction, so ending values are approximate

## All cor, lit, and grid files exist!
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Mean Phenotype Whole Simulation

First, I will look at a plot of how the mean phenotype of the entire population of newts and snakes changes overtime. Each of these plots has three colored lines, red for the mean newt phenotype, blue for the mean snake phenotype, and black for the difference between mean snake and mean newt phenotype. There are 11 line per color that represent the different interaction rates that I ran. Note this is a mean for the entire population. Mutational variance increases for the snakes as you go down the figure (top to bottom) and increases for the newts as you go across (left to right).

Correlation Histograms

In order to understand how spatial correlations where changing with time I took 5,000 generation time slices to look at all four trials correlation values. Each color is a different trial per GA combination. The histogram values are stacked. This section only looks at the 5 sections.

Plot 1

Plot 2

Plot 3

Plot 4

Plot 5

Plot 6

Plot 7

Plot 8

Plot 9

Plot 10

Phenotype Correlation across time

Next, we will examine three randomly chosen plots from both the 5 section and 7 section experiment. Time (in generations) in on the x-axis and both mean phenotype and phenotype spatial correlation in on the y-axis. Newt whole population mean phenotype is red, while snake mean phenotype is blue. The pink line is the phenotype spatial correlation.

Random 1 (5 sec)

Random 2 (5 sec)

Random 3 (5 sec)

Population Size Correlation across time

Random 1

Random 2

Random 3

What happens over time (looking at the beginning and late part of my simulations)

Pheno Beginning 0.01

Pheno Beginning 0.025

Pheno Beginning 0.05

Pheno Beginning 0.075

Pheno Beginning 0.10

Pheno Beginning 0.125

Pheno Beginning 0.15

Pheno Beginning 0.20

Pheno Beginning 0.25

Pheno Beginning 0.30

Pheno Beginning 0.35

Pheno End 0.01

Pheno End 0.025

Pheno End 0.05

Pheno End 0.075

Pheno End 0.10

Pheno End 0.125

Pheno End 0.15

Pheno End 0.20

Pheno End 0.25

Pheno End 0.30

Pheno End 0.35

Heatmap

interrate: Population Size (Early)

interrate: Population Size (EM1)

interrate: Population Size (EM2)

interrate: Population Size (EM3)

interrate: Population Size (EM4)

interrate: Population Size (Mid)

interrate: Population Size (ML1)

interrate: Population Size (ML2)

interrate: Population Size (ML3)

interrate: Population Size (Late)

interrate: Phenotype (Early)

interrate: Phenotype (EM1)

interrate: Phenotype (EM2)

interrate: Phenotype (EM3)

interrate: Phenotype (EM4)

interrate: Phenotype (Mid)

interrate: Phenotype (ML1)

interrate: Phenotype (ML2)

interrate: Phenotype (ML3)

interrate: Phenotype (Late)

##Grid {.tabset}

Grid Figs

0.01

## [1] -0.05766393

0.025

## [1] 0.01880521

0.05

## [1] -0.06008882

0.075

## [1] -0.02381402

0.10

## [1] 0.5744616

0.125

0.15

## [1] 0.07042592

0.20

## [1] -0.3938411

0.25

0.30

0.35

Grid Figs 2

0.01

## [1] 0.417992

0.025

## [1] -0.07059617

0.05

## [1] 0.06019905

0.075

## [1] 0.09767028

0.10

## [1] -0.5766155

0.125

0.15

0.20

0.25

## [1] -0.2795285

0.30

0.35

## [1] -0.6610814

Grid Figs

0.01

## [1] -0.1749074

0.025

## [1] -0.03684979

0.05

## [1] -0.03716862

0.075

0.10

0.125

0.15

0.20

0.25

0.30

0.35